How do I change a bucket to use coldline storage
I uploaded close to 1000 bams to a FireCloud bucket and then was able to run the analysis that I needed on them. I was wondering how I how I can go about either changing this bucket to use coldline...
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Getting internal server error when trying to access specific run output info...
When clicking on "View" for any of rows pictured above, getting following server error: Any insights into what might be happening?
View ArticleHow to link Firecloud account to eRA commons for TCGA controlled access?
I'm looking to use the new CGA WES workflow, and specifically the one with TCGA PoN (broad-fc-getzlab-workflows/CGA_WES_Characterization_TCGAControlledAccess) how do we link our Firecloud account to...
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"View" for workflow details does not show anything
Hello, I have a workspace with an authorized domain setting. For some reason, I could not see any workflow details on the Monitor tab: There are other workspaces with and without authorized domain...
View ArticleMutect2 WES intervals
Hi, this is my first time analyzing WES data using Firecloud and I have a question about the intervals for WES data. I ran the Mutect2-GATK4 method on a set of single samples (WES) using the...
View ArticleUnable to launch HailContext from Firecloud Notebook
Dear Firecloud team, The Hail team referred me to you regarding my issues regarding launching Hail from the Firecloud notebook, which is currently not working as the Apache version that is used on the...
View ArticleMutect 1 vs Mutect 2
Hello I am interested in running mutect on wgs. I understand that for snvs mutect 1 is better to run than mutect 2 as mutect 2 has only been validated for indels (or at least mutect 1 is pretty...
View ArticleTask takes 2 hours in FireCloud, seconds on my laptop
In my workflow https://portal.firecloud.org/#workspaces/jianshu-projects/181217_JB_scATAC_v1/monitor/2fd7591f-964f-4b06-a504-41de4122156d/62acb6bd-298e-4972-852e-d2998af594d6, I scatter running bowtie...
View Articlejava.lang.IllegalArgumentException: Could not build the path
Hi, I am new to FireCloud and trying to run my first workflow. Specifically, I am trying to launch the haplotypecaller-gvcf-gatk4 workflow using a BAM file (and index) I have already generated. I...
View Articlejoint-discovery-gatk4-local.wdl uses deprecated output syntax
In the GitHub-provided, official WDL files for running GATK, the "local" version of joint discovery uses a deprecated form of declaring outputs, which prevents it from being run as a subworkflow....
View Article"The Google bucket associated with this workspace is currently unavailable"
Hey there, I encounter the above error message while viewing a workspace to which I have Writer level access. Is there a fix to this? The workspace name is: "nci-mxhe-bi-org/cellranger_references"...
View Article"glob(path, pattern) not implemented yet"
Hi there, I'm trying to run a wdl workflow using globs on Cromwell 3.6. A simple command like: Array[File] input_bams = glob("*.bam") Generates the following error: [2019-01-07 15:53:42,52]...
View ArticlePlease elaborate on "institutional affiliation" field, required for registration
Please elaborate on "institutional affiliation" field, required for registration
View ArticleCluster stuck on "Creating"
Hi- I tried to start a cluster through FireCloud's notebook feature this morning. Through the FireCloud UI, the cluster has been stuck on "Creating" for ~4 hours. This same status is reflected using...
View ArticleA USER ERROR has occurred: Traversal by intervals was requested but some...
Hi Team, We are running Cromwell on AWS and running five-dollar-genome-analysis-pipeline-master using GATK toolset. After resolving couple issues related to missing files, NIO etc, we are facing yet...
View ArticleHow to restart a wdl workflow task from where it failed on google cloud
Hi , I'm trying to run a scatter wdl workflow on google cloud through cromwell , how do I restart the workflow from where it stopped? Thanks, Archana
View ArticleGATK "bwa_commandline" variable settings and comparisons to Bowtie2
Hi there, I've been working on improving a workflow for processing data for my lab, and I wanted to compare the workflow we have set out to some of GATK's best practices workflows. We are currently...
View ArticlePySpark2 Notebooks in Firecloud to use Hail.
Hello, I am trying to use Notebooks integrated in the Firecloud. When i see the documentation there was a line that mentioned to use PySpark2 notebooks to use Hail. Unfortunately when I was tryin to...
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Queued in Cromwell and Error: empty on next iterator
Hi team, Jobs have been queued in Cromwell for a couple of hours for myself and multiple other users. The following error comes up when I tried to relaunch jobs to see if that would help (image)
View ArticleWhen I use CromWell to run a WDL, I got error like Docker lookup failed
Here is my command: java -Dconfig.file=myCromwell.conf -jar cromwell-34.jar run processing-for-variant-discovery-gatk4.wdl --inputs input.json I got following errors: [warn]...
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